🧬 CDR Dynamics Analysis Dashboard

Specialized analysis for antibody CDR regions based on 4G6K gevokizumab structure

🧬 CDR Residue Information (4G6K Gevokizumab)

Total CDR Residues: 26
CDR Residues: 31, 32, 33, 34, 35, 52, 54, 55, 56, 100, 101, 102, 103, 104, 105, 106, 151, 152, 169, 170, 173, 211, 212, 213, 214, 216
43
CDR Analyses
10000.0
Simulation Time (ns)
26
CDR Residues
🏗️ CDR Structural Stability
20.0
F
CDR backbone preservation during simulation
🌊 CDR Flexibility
44.2
F
Optimal flexibility for antigen binding
🔓 CDR Accessibility
0.0
F
Solvent accessibility of binding regions
📦 CDR Compactness
95.0
A+
Structural compactness of CDR regions
⚖️ Relative Performance
50.0
F
CDR dynamics relative to protein backbone
🔗 Binding Dynamics
66.5
C
Hydrogen bonding and interaction stability
🎯 Overall CDR Quality
53.1
F
Comprehensive CDR dynamics assessment

CDR Quality Assessment Radar

💡 CDR Analysis Insights

  • ⚠️ Moderate CDR quality - Some CDR stability issues detected, consider analysis of specific loops
  • ⚠️ CDR flexibility concerns - CDR regions may be too rigid or overly flexible for optimal binding
  • ⚠️ CDR accessibility issues - Reduced surface accessibility may affect antigen binding
  • ⚠️ CDR structural instability - High RMSD in CDR regions suggests conformational changes
  • 💡 Analysis tip: Focus on individual CDR loops (H1, H2, H3, L1, L2, L3) for detailed loop-specific behavior assessment

📊 CDR-Focused Analysis Results

🗂️ CDR Analysis Overview

GROMACS Energies Unknown

📁 File: density.xvg
🔬 Analysis Type: Unknown
📈 Data points: 251
⚙️ GROMACS command: gmx energy -f npt.edr -o density.xvg

Radius of gyration (total and around axes) Cdr Gyration

📁 File: gyrate_CDR_All.xvg
🔬 Analysis Type: Cdr Gyration
📈 Data points: 5,001
⚙️ GROMACS command: gmx gyrate -s md_0_10.tpr -f dynamic-nopbc.xtc -o gyrate_CDR_All.xvg -n index_cdr.ndx

Radius of gyration (total and around axes) Cdr Gyration

📁 File: gyrate_CDR_H1.xvg
🔬 Analysis Type: Cdr Gyration
📈 Data points: 5,001
⚙️ GROMACS command: gmx gyrate -s md_0_10.tpr -f dynamic-nopbc.xtc -o gyrate_CDR_H1.xvg -n index_cdr.ndx

Radius of gyration (total and around axes) Cdr Gyration

📁 File: gyrate_CDR_H1_comp.xvg
🔬 Analysis Type: Cdr Gyration
📈 Data points: 5,001
⚙️ GROMACS command: gmx gyrate -s md_0_10.tpr -f dynamic-nopbc.xtc -o gyrate_CDR_H1_comp.xvg -n index_cdr.ndx

Radius of gyration (total and around axes) Cdr Gyration

📁 File: gyrate_CDR_H2.xvg
🔬 Analysis Type: Cdr Gyration
📈 Data points: 5,001
⚙️ GROMACS command: gmx gyrate -s md_0_10.tpr -f dynamic-nopbc.xtc -o gyrate_CDR_H2.xvg -n index_cdr.ndx

Radius of gyration (total and around axes) Cdr Gyration

📁 File: gyrate_CDR_H2_comp.xvg
🔬 Analysis Type: Cdr Gyration
📈 Data points: 5,001
⚙️ GROMACS command: gmx gyrate -s md_0_10.tpr -f dynamic-nopbc.xtc -o gyrate_CDR_H2_comp.xvg -n index_cdr.ndx

Radius of gyration (total and around axes) Cdr Gyration

📁 File: gyrate_CDR_H3.xvg
🔬 Analysis Type: Cdr Gyration
📈 Data points: 5,001
⚙️ GROMACS command: gmx gyrate -s md_0_10.tpr -f dynamic-nopbc.xtc -o gyrate_CDR_H3.xvg -n index_cdr.ndx

Radius of gyration (total and around axes) Cdr Gyration

📁 File: gyrate_CDR_H3_comp.xvg
🔬 Analysis Type: Cdr Gyration
📈 Data points: 5,001
⚙️ GROMACS command: gmx gyrate -s md_0_10.tpr -f dynamic-nopbc.xtc -o gyrate_CDR_H3_comp.xvg -n index_cdr.ndx

Radius of gyration (total and around axes) Cdr Gyration

📁 File: gyrate_CDR_L1.xvg
🔬 Analysis Type: Cdr Gyration
📈 Data points: 5,001
⚙️ GROMACS command: gmx gyrate -s md_0_10.tpr -f dynamic-nopbc.xtc -o gyrate_CDR_L1.xvg -n index_cdr.ndx

Radius of gyration (total and around axes) Cdr Gyration

📁 File: gyrate_CDR_L1_comp.xvg
🔬 Analysis Type: Cdr Gyration
📈 Data points: 5,001
⚙️ GROMACS command: gmx gyrate -s md_0_10.tpr -f dynamic-nopbc.xtc -o gyrate_CDR_L1_comp.xvg -n index_cdr.ndx

Radius of gyration (total and around axes) Cdr Gyration

📁 File: gyrate_CDR_L2.xvg
🔬 Analysis Type: Cdr Gyration
📈 Data points: 5,001
⚙️ GROMACS command: gmx gyrate -s md_0_10.tpr -f dynamic-nopbc.xtc -o gyrate_CDR_L2.xvg -n index_cdr.ndx

Radius of gyration (total and around axes) Cdr Gyration

📁 File: gyrate_CDR_L2_comp.xvg
🔬 Analysis Type: Cdr Gyration
📈 Data points: 5,001
⚙️ GROMACS command: gmx gyrate -s md_0_10.tpr -f dynamic-nopbc.xtc -o gyrate_CDR_L2_comp.xvg -n index_cdr.ndx

Radius of gyration (total and around axes) Cdr Gyration

📁 File: gyrate_CDR_L3.xvg
🔬 Analysis Type: Cdr Gyration
📈 Data points: 5,001
⚙️ GROMACS command: gmx gyrate -s md_0_10.tpr -f dynamic-nopbc.xtc -o gyrate_CDR_L3.xvg -n index_cdr.ndx

Radius of gyration (total and around axes) Cdr Gyration

📁 File: gyrate_CDR_L3_comp.xvg
🔬 Analysis Type: Cdr Gyration
📈 Data points: 5,001
⚙️ GROMACS command: gmx gyrate -s md_0_10.tpr -f dynamic-nopbc.xtc -o gyrate_CDR_L3_comp.xvg -n index_cdr.ndx

Radius of gyration (total and around axes) Protein Gyration

📁 File: gyrate_protein.xvg
🔬 Analysis Type: Protein Gyration
📈 Data points: 5,001
⚙️ GROMACS command: gmx gyrate -s md_0_10.tpr -f dynamic-nopbc.xtc -o gyrate_protein.xvg -n index_cdr.ndx

Hydrogen Bonds Hydrogen Bonds

📁 File: hbond_protein.xvg
🔬 Analysis Type: Hydrogen Bonds
📈 Data points: 5,001
⚙️ GROMACS command: gmx hbond -s md_0_10.tpr -f dynamic-nopbc.xtc -num hbond_protein.xvg -n index_cdr.ndx

GROMACS Energies Potential Energy

📁 File: potential.xvg
🔬 Analysis Type: Potential Energy
📈 Data points: 283
⚙️ GROMACS command: gmx energy -f em.edr -o potential.xvg

GROMACS Energies Pressure

📁 File: pressure.xvg
🔬 Analysis Type: Pressure
📈 Data points: 251
⚙️ GROMACS command: gmx energy -f npt.edr -o pressure.xvg

r_31_32_33_34_35_52_54_55_56_100_101_102_103_104_105_106_151_152_169_170_173_211_212_213_214_216 after lsq fit to r_31_32_33_34_35_52_54_55_56_100_101_102_103_104_105_106_151_152_169_170_173_211_212_213_214_216 Cdr Rmsd

📁 File: rmsd_CDR_All.xvg
🔬 Analysis Type: Cdr Rmsd
📈 Data points: 5,001
⚙️ GROMACS command: gmx rms -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsd_CDR_All.xvg -n index_cdr.ndx -tu ns

r_169_170_173 after lsq fit to r_169_170_173 Cdr Rmsd

📁 File: rmsd_CDR_H1.xvg
🔬 Analysis Type: Cdr Rmsd
📈 Data points: 5,001
⚙️ GROMACS command: gmx rms -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsd_CDR_H1.xvg -n index_cdr.ndx -tu ns

r_211_212_213_214_216 after lsq fit to r_211_212_213_214_216 Cdr Rmsd

📁 File: rmsd_CDR_H2.xvg
🔬 Analysis Type: Cdr Rmsd
📈 Data points: 5,001
⚙️ GROMACS command: gmx rms -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsd_CDR_H2.xvg -n index_cdr.ndx -tu ns

r_31_32_33_34_35_52_54_55_56_100_101_102_103_104_105_106_151_152_169_170_173_211_212_213_214_216 after lsq fit to r_31_32_33_34_35_52_54_55_56_100_101_102_103_104_105_106_151_152_169_170_173_211_212_213_214_216 Cdr Rmsd

📁 File: rmsd_CDR_H3.xvg
🔬 Analysis Type: Cdr Rmsd
📈 Data points: 5,001
⚙️ GROMACS command: gmx rms -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsd_CDR_H3.xvg -n index_cdr.ndx -tu ns

r_52_54_55_56 after lsq fit to r_52_54_55_56 Cdr Rmsd

📁 File: rmsd_CDR_L1.xvg
🔬 Analysis Type: Cdr Rmsd
📈 Data points: 5,001
⚙️ GROMACS command: gmx rms -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsd_CDR_L1.xvg -n index_cdr.ndx -tu ns

r_100_101_102_103_104_105_106 after lsq fit to r_100_101_102_103_104_105_106 Cdr Rmsd

📁 File: rmsd_CDR_L2.xvg
🔬 Analysis Type: Cdr Rmsd
📈 Data points: 5,001
⚙️ GROMACS command: gmx rms -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsd_CDR_L2.xvg -n index_cdr.ndx -tu ns

r_151_152 after lsq fit to r_151_152 Cdr Rmsd

📁 File: rmsd_CDR_L3.xvg
🔬 Analysis Type: Cdr Rmsd
📈 Data points: 5,001
⚙️ GROMACS command: gmx rms -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsd_CDR_L3.xvg -n index_cdr.ndx -tu ns

r_31_32_33_34_35_52_54_55_56_100_101_102_103_104_105_106_151_152_169_170_173_211_212_213_214_216 after lsq fit to Backbone Rmsd Comparison

📁 File: rmsd_comparison.xvg
🔬 Analysis Type: Rmsd Comparison
📈 Data points: 5,001
⚙️ GROMACS command: gmx rms -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsd_comparison.xvg -n index_cdr.ndx -tu ns

Backbone after lsq fit to Backbone Protein Rmsd

📁 File: rmsd_protein.xvg
🔬 Analysis Type: Protein Rmsd
📈 Data points: 5,001
⚙️ GROMACS command: gmx rms -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsd_protein.xvg -n index_cdr.ndx -tu ns

RMS fluctuation Cdr Rmsf

📁 File: rmsf_CDR_All.xvg
🔬 Analysis Type: Cdr Rmsf
📈 Data points: 49
⚙️ GROMACS command: gmx rmsf -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsf_CDR_All.xvg -n index_cdr.ndx -res

RMS fluctuation Cdr Rmsf

📁 File: rmsf_CDR_H1.xvg
🔬 Analysis Type: Cdr Rmsf
📈 Data points: 6
⚙️ GROMACS command: gmx rmsf -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsf_CDR_H1.xvg -n index_cdr.ndx -res

RMS fluctuation Cdr Rmsf

📁 File: rmsf_CDR_H1_comp.xvg
🔬 Analysis Type: Cdr Rmsf
📈 Data points: 4
⚙️ GROMACS command: gmx rmsf -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsf_CDR_H1_comp.xvg -n index_cdr.ndx -res

RMS fluctuation Cdr Rmsf

📁 File: rmsf_CDR_H2.xvg
🔬 Analysis Type: Cdr Rmsf
📈 Data points: 7
⚙️ GROMACS command: gmx rmsf -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsf_CDR_H2.xvg -n index_cdr.ndx -res

RMS fluctuation Cdr Rmsf

📁 File: rmsf_CDR_H2_comp.xvg
🔬 Analysis Type: Cdr Rmsf
📈 Data points: 6
⚙️ GROMACS command: gmx rmsf -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsf_CDR_H2_comp.xvg -n index_cdr.ndx -res

RMS fluctuation Cdr Rmsf

📁 File: rmsf_CDR_H3.xvg
🔬 Analysis Type: Cdr Rmsf
📈 Data points: 49
⚙️ GROMACS command: gmx rmsf -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsf_CDR_H3.xvg -n index_cdr.ndx -res

RMS fluctuation Cdr Rmsf

📁 File: rmsf_CDR_H3_comp.xvg
🔬 Analysis Type: Cdr Rmsf
📈 Data points: 7
⚙️ GROMACS command: gmx rmsf -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsf_CDR_H3_comp.xvg -n index_cdr.ndx -res

RMS fluctuation Cdr Rmsf

📁 File: rmsf_CDR_L1.xvg
🔬 Analysis Type: Cdr Rmsf
📈 Data points: 8
⚙️ GROMACS command: gmx rmsf -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsf_CDR_L1.xvg -n index_cdr.ndx -res

RMS fluctuation Cdr Rmsf

📁 File: rmsf_CDR_L1_comp.xvg
🔬 Analysis Type: Cdr Rmsf
📈 Data points: 10
⚙️ GROMACS command: gmx rmsf -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsf_CDR_L1_comp.xvg -n index_cdr.ndx -res

RMS fluctuation Cdr Rmsf

📁 File: rmsf_CDR_L2.xvg
🔬 Analysis Type: Cdr Rmsf
📈 Data points: 14
⚙️ GROMACS command: gmx rmsf -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsf_CDR_L2.xvg -n index_cdr.ndx -res

RMS fluctuation Cdr Rmsf

📁 File: rmsf_CDR_L2_comp.xvg
🔬 Analysis Type: Cdr Rmsf
📈 Data points: 8
⚙️ GROMACS command: gmx rmsf -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsf_CDR_L2_comp.xvg -n index_cdr.ndx -res

RMS fluctuation Cdr Rmsf

📁 File: rmsf_CDR_L3.xvg
🔬 Analysis Type: Cdr Rmsf
📈 Data points: 4
⚙️ GROMACS command: gmx rmsf -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsf_CDR_L3.xvg -n index_cdr.ndx -res

RMS fluctuation Cdr Rmsf

📁 File: rmsf_CDR_L3_comp.xvg
🔬 Analysis Type: Cdr Rmsf
📈 Data points: 14
⚙️ GROMACS command: gmx rmsf -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsf_CDR_L3_comp.xvg -n index_cdr.ndx -res

RMS fluctuation Protein Rmsf

📁 File: rmsf_protein.xvg
🔬 Analysis Type: Protein Rmsf
📈 Data points: 432
⚙️ GROMACS command: gmx rmsf -s md_0_10.tpr -f dynamic-nopbc.xtc -o rmsf_protein.xvg -n index_cdr.ndx -res

Solvent Accessible Surface Protein Sasa

📁 File: sasa_protein.xvg
🔬 Analysis Type: Protein Sasa
📈 Data points: 5,001
⚙️ GROMACS command: gmx sasa -s md_0_10.tpr -f dynamic-nopbc.xtc -o sasa_protein.xvg -n index_cdr.ndx

GROMACS Energies Temperature

📁 File: temperature.xvg
🔬 Analysis Type: Temperature
📈 Data points: 251
⚙️ GROMACS command: gmx energy -f nvt.edr -o temperature.xvg

🧬 CDR Dynamics Analysis Dashboard • Generated on 2025-07-09 05:47:20

Specialized for 4G6K Gevokizumab CDR Analysis • Powered by Python & Plotly.js

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